1. Tests of diversity
2. Tests of tree shape
3. Tests of evolutionary rates
Test: is there less genetic diversity than expected?
Influenza phylogeny and effective number of infections
Coalescent rates in flu and measles
Selective sweeps purge diversity
Test: is the tree shape different from the neutral expectation?
Tajima's D statistic summarizes deviation from neutrality
Influenza has negative Tajima's D
Test: is there an overabundance of fixed non-synonymous mutations?
"Trunk" branches show an excess of non-synonymous change at epitope sites in influenza
Abundance of green epitope mutations on phylogeny trunk, relative to blue synonymous and red non-epitope mutations
Can be extended to look at relationship between mutations and clade growth
